David Vondracek of the Czech Republic claimed bronze in 48:34.
Briton Stone said: 'I made my move, but the Italian (Farroni) stayed with me. It was so hard.
'It makes it better to win today because it was so disappointing not winning in the Time Trial.
'Compared to Beijing, the competition was so much better, it's good. It pushes me. It makes it a much better sport.'
There was also joy for Canada's Robbi Weldon and her pilot Lyne Bessette in the second race, as they won women's Individual B gold by 33 seconds from Spanish pair Josefa Benitez Guzman and her pilot Maria Noriega.
The Netherlands' Kathrin Goeken and Kim van Dijk claimed bronze in a sprint for third place, just edging out four other pairings.
Ivano Pizzi and guide Lucca Pizzi won Individual B Road Race gold for Italy, with the silver going to Poland's Krzysztof Kosikowski and Artur Korc. Slovakian pair Vladislav Janovjak and Robert Mitosinka won bronze.
In the Mixed H1-4 Team Relay, the USA took gold, followed by Italy and Switzerland.